Fix 0.4.0dev tests

.github/workflows/test_and_deploy.yml

@@ -11,7 +11,7 @@ on:
       - "*"
   pull_request:
     branches:
-      - main
+      - "*"
   workflow_dispatch:
 
 jobs:

recOrder/cli/apply_inverse_transfer_function.py

@@ -109,9 +109,10 @@ def apply_inverse_transfer_function_cli(
     )
 
     # Load data
+    tczyx_uint16_numpy = input_dataset.data.oindex[:, channel_indices]
     tczyx_data = torch.tensor(
-        input_dataset.data.oindex[:, channel_indices], dtype=torch.float32
-    )
+        np.int32(tczyx_uint16_numpy), dtype=torch.float32
+    )  # convert to np.int32 (torch doesn't accept np.uint16), then convert to tensor float32
 
     # Prepare background dataset
     if settings.birefringence is not None:
@@ -164,7 +165,7 @@ def apply_inverse_transfer_function_cli(
         echo_headline("Reconstructing phase...")
 
         # check data shapes
-        if input_dataset.data.shape[1] != 1:
+        if tczyx_data.shape[1] != 1:
             raise ValueError(
                 "You have requested a phase-only reconstruction, but the input dataset has more than one channel."
             )
@@ -385,10 +386,10 @@ def apply_inv_tf(
     """
     Apply an inverse transfer function to a dataset using a configuration file.
 
-    See /examples/settings/ for example configuration files.
+    See /examples for example configuration files.
 
     Example usage:\n
-    $ recorder apply-inv-tf input.zarr/0/0/0 transfer-function.zarr -c /examples/settings/birefringence.yml -o output.zarr
+    $ recorder apply-inv-tf input.zarr/0/0/0 transfer-function.zarr -c /examples/birefringence.yml -o output.zarr
     """
     apply_inverse_transfer_function_cli(
         input_data_path, transfer_function_path, config_path, output_path

recOrder/cli/compute_transfer_function.py

@@ -211,9 +211,9 @@ def compute_tf(input_data_path, config_path, output_path):
     """
     Compute a transfer function using a dataset and configuration file.
 
-    See /examples/settings/ for example configuration files.
+    See /examples/ for example configuration files.
 
     Example usage:\n
-    $ recorder compute-tf input.zarr/0/0/0 -c /examples/settings/birefringence.yml -o transfer_function.zarr
+    $ recorder compute-tf input.zarr/0/0/0 -c /examples/birefringence.yml -o transfer_function.zarr
     """
     compute_transfer_function_cli(input_data_path, config_path, output_path)

recOrder/cli/reconstruct.py

@@ -23,10 +23,10 @@ def reconstruct(input_data_path, config_path, output_path):
     convenience function for a `compute-tf` call followed by a `apply-inv-tf`
     call.
 
-    See /examples/settings/ for example configuration files.
+    See /examples for example configuration files.
 
     Example usage:\n
-    $ recorder reconstruct input.zarr/0/0/0 -c /examples/settings/birefringence.yml -o output.zarr
+    $ recorder reconstruct input.zarr/0/0/0 -c /examples/birefringence.yml -o output.zarr
     """
 
     # Handle transfer function path

recOrder/tests/cli_tests/test_compute_tf.py

@@ -11,17 +11,19 @@
 
 def test_compute_transfer(tmp_path, input_zarr):
     recon_settings = settings.ReconstructionSettings(
-            input_channel_names=[f"State{i}" for i in range(5)],
-            reconstruction_dimension=3,
-            birefringence=settings.BirefringenceSettings(),
-            phase=settings.PhaseSettings(),
-        )
+        input_channel_names=[f"State{i}" for i in range(4)],
+        reconstruction_dimension=3,
+        birefringence=settings.BirefringenceSettings(),
+        phase=settings.PhaseSettings(),
+    )
     config_path = tmp_path / "test.yml"
     utils.model_to_yaml(recon_settings, config_path)
 
     path, _ = input_zarr
     runner = CliRunner()
-    result = runner.invoke(cli, ["compute-tf", str(path), "-c", str(config_path)])
+    result = runner.invoke(
+        cli, ["compute-tf", str(path), "-c", str(config_path)]
+    )
     assert result.exit_code == 0
 
 
@@ -45,10 +47,10 @@ def test_compute_transfer_blank_output():
 
 def test_compute_transfer_output_file(tmp_path, input_zarr):
     recon_settings = settings.ReconstructionSettings(
-            input_channel_names=["TEST"],
-            reconstruction_dimension=3,
-            phase=settings.PhaseSettings(),
-        )
+        input_channel_names=["BF"],
+        reconstruction_dimension=3,
+        phase=settings.PhaseSettings(),
+    )
     config_path = tmp_path / "test.yml"
     utils.model_to_yaml(recon_settings, config_path)
 

recOrder/tests/cli_tests/test_reconstruct.py

@@ -49,12 +49,14 @@ def test_reconstruct(tmp_path):
         tf_path = input_path.with_name("tf.zarr")
         runner.invoke(
             cli,
-            "compute-tf "
-            + str(input_path)
-            + " -c "
-            + str(config_path)
-            + " -o "
-            + str(tf_path),
+            [
+                "compute-tf",
+                str(input_path),
+                "-c",
+                str(config_path),
+                "-o",
+                str(tf_path),
+            ],
         )
         assert tf_path.exists()
 
@@ -63,14 +65,15 @@ def test_reconstruct(tmp_path):
 
         result_inv = runner.invoke(
             cli,
-            "apply-inv-tf "
-            + str(input_path)
-            + " "
-            + str(tf_path)
-            + " -c "
-            + str(config_path)
-            + " -o "
-            + str(result_path),
+            [
+                "apply-inv-tf",
+                str(input_path),
+                str(tf_path),
+                "-c",
+                str(config_path),
+                "-o",
+                str(result_path),
+            ],
         )
         assert result_path.exists()
         assert result_inv.exit_code == 0

recOrder/tests/cli_tests/test_settings.py

@@ -9,7 +9,7 @@ def test_reconstruction_settings():
     s = settings.ReconstructionSettings(
         birefringence=settings.BirefringenceSettings()
     )
-    assert len(s.input_channel_names) == 5
+    assert len(s.input_channel_names) == 4
     assert s.birefringence.apply_inverse.background_path == ""
     assert s.phase == None
     assert s.fluorescence == None

recOrder/tests/conftest.py

@@ -12,9 +12,9 @@ def input_zarr(tmp_path):
         path,
         layout="fov",
         mode="w",
-        channel_names=["None"],
+        channel_names=[f"State{i}" for i in range(4)] + ["BF"],
     )
-    dataset.create_zeros("0", (2, 1, 4, 5, 6), dtype=np.float32)
+    dataset.create_zeros("0", (2, 5, 4, 5, 6), dtype=np.uint16)
     yield path, dataset
 
 
@@ -25,7 +25,10 @@ def birefringence_phase_recon_settings_function(tmp_path):
         phase=settings.PhaseSettings(),
     )
     dataset = open_ome_zarr(
-        tmp_path, layout="fov", mode="w", channel_names=["None"]
+        tmp_path,
+        layout="fov",
+        mode="w",
+        channel_names=[f"State{i}" for i in range(4)],
     )
     yield recon_settings, dataset
 
@@ -37,6 +40,9 @@ def fluorescence_recon_settings_function(tmp_path):
         fluorescence=settings.FluorescenceSettings(),
     )
     dataset = open_ome_zarr(
-        tmp_path, layout="fov", mode="w", channel_names=["None"]
+        tmp_path,
+        layout="fov",
+        mode="w",
+        channel_names=[f"State{i}" for i in range(4)],
     )
     yield recon_settings, dataset

setup.cfg

@@ -37,7 +37,7 @@ python_requires = >=3.9
 setup_requires = setuptools_scm
 # add your package requirements here
 install_requires =
-	waveorder==2.0.0rc0
+	waveorder==2.0.0rc1
 	pycromanager==0.27.2
 	click>=8.0.1
 	natsort>=7.1.1